BrainPET

HI

$/!\$ This page is only to process PET-MR data acquired using BrainPET (Bay 6) scanner at the Athinoula A. Martinos Center for Biomedical Imaging.

Aether-Mirror Version

This version mirrors the attenuation map generation and reconstruction algorithms that were used on Aether. We recommend to use this version only for continuation studies.

PseudoCT mu-map generation

This function generates pseudoCT mu-map using SPM8 atlas-based method (David Izquierdo-Garcia et al.)

For DICOM input:

perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR/MPRAGE -f 107000-000005-000001.dcm -c 0

For NIFTI input

perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR_PET -f cp_iso_mprage.nii -c 0

IMP1: The r-l flip is applied only to .dcm input but not to .nii input (see Imp2)
IMP2: If you input a nifti file, it should be named as cp_iso_mprage.nii and it should be r-l flipped (i.e., it is the output of a previously ran pesudo CT).

Supporting Functions

Denoise MPRAGE

perl brainPET_denoise_mprage.pl -i /<DIR>/<SUBJID>/MR_PET/cp_iso_mprage.nii -t 25 -s 0

ifile2nifti

perl brainPET_ifile2nifti.pl -i /<DIR>/file.i

-  ⇤ ← Revision 2 as of 2019-06-20 14:18:51 → 
  Size: 0
  Editor: MorganFogarty
  Comment:
+   ← Revision 15 as of 2021-02-17 19:55:13 → ⇥
  Size: 2042
  Editor: MeenaMakary
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+## page was renamed from brainPET
## page was renamed from MyNewPage
## Please edit system and help pages ONLY in the master wiki!
## For more information, please see MoinMoin:MoinDev/Translation.
## IMPORTANT NOTE:
## When you use this page as a template for creating your project page:
##  * please remove all lines starting with two hashes (##)
##  * except the acl line, please keep that, but remove one hash, so it reads #acl ...
##  * fix the acl line so it has the correct page instead of the sample Project/...Group
##acl Project/AdminGroup:admin,read,write,delete,revert Project/ReadWriteGroup:read,write Project/ReadGroup:read
##master-page:Unknown-Page
##master-date:Unknown-Date
#format wiki
#language en
'''Index'''
<<TableOfContents(2)>>

= BrainPET =
{{{
HI
}}}

---- /!\ '''This page is only to process PET-MR data acquired using BrainPET (Bay 6) scanner at the Athinoula A. Martinos Center for Biomedical Imaging.''' ---- 
 
= Aether-Mirror Version =
This version mirrors the attenuation map generation and reconstruction algorithms that were used on Aether. We recommend to use this version only for continuation studies. 

== PseudoCT mu-map generation ==
This function generates pseudoCT mu-map using SPM8 atlas-based method (David Izquierdo-Garcia et al.)

 * For DICOM input:
{{{
perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR/MPRAGE -f 107000-000005-000001.dcm -c 0
}}}

 * For NIFTI input
{{{
perl brainPET_pCT_AeMir.pl -i /<DIR>/<SUJID>/MR_PET -f cp_iso_mprage.nii -c 0
}}}

 * IMP1: The r-l flip is applied only to .dcm input but not to .nii input (see Imp2)
 * IMP2: If you input a nifti file, it should be named as cp_iso_mprage.nii and it should be r-l flipped (i.e., it is the output of a previously ran pesudo CT).

= Supporting Functions =
== Denoise MPRAGE ==
{{{
perl brainPET_denoise_mprage.pl -i /<DIR>/<SUBJID>/MR_PET/cp_iso_mprage.nii -t 25 -s 0
}}}

== ifile2nifti ==
{{{
perl brainPET_ifile2nifti.pl -i /<DIR>/file.i
}}}

= Development Version =